2YBR

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4.
Crystal Properties
Matthew coefficientSolvent content
2.6153

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.844α = 90
b = 104.494β = 90
c = 152.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH MX-300MIRRORS2009-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.5546.299.90.16.46.437179232.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.691000.332.36.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB2.5545.7235277185899.90.194550.191830.24673RANDOM32.766
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.020.630.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.901
r_dihedral_angle_4_deg22.144
r_dihedral_angle_3_deg14.996
r_scangle_it7.155
r_dihedral_angle_1_deg5.856
r_scbond_it5.184
r_mcangle_it4.702
r_mcbond_it3.344
r_angle_refined_deg1.257
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.901
r_dihedral_angle_4_deg22.144
r_dihedral_angle_3_deg14.996
r_scangle_it7.155
r_dihedral_angle_1_deg5.856
r_scbond_it5.184
r_mcangle_it4.702
r_mcbond_it3.344
r_angle_refined_deg1.257
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_mcangle_other
r_gen_planes_other
r_scbond_other
r_nbd_refined
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6721
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing